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- PDB-7v1k: Apo structure of sNASP core -

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Basic information

Entry
Database: PDB / ID: 7v1k
TitleApo structure of sNASP core
ComponentsIsoform 2 of Nuclear autoantigenic sperm protein
KeywordsCHAPERONE / histone chaperone
Function / homologyIsoform 2 of Nuclear autoantigenic sperm protein
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.287 Å
AuthorsBao, H. / Huang, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2018YFC1004500 China
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: NASP maintains histone H3-H4 homeostasis through two distinct H3 binding modes.
Authors: Bao, H. / Carraro, M. / Flury, V. / Liu, Y. / Luo, M. / Chen, L. / Groth, A. / Huang, H.
History
DepositionAug 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jun 1, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 2 of Nuclear autoantigenic sperm protein


Theoretical massNumber of molelcules
Total (without water)28,2621
Polymers28,2621
Non-polymers00
Water00
1
A: Isoform 2 of Nuclear autoantigenic sperm protein

A: Isoform 2 of Nuclear autoantigenic sperm protein


Theoretical massNumber of molelcules
Total (without water)56,5252
Polymers56,5252
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/31
Buried area3860 Å2
ΔGint-35 kcal/mol
Surface area23600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.358, 95.358, 206.229
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Isoform 2 of Nuclear autoantigenic sperm protein / NASP / NASP


Mass: 28262.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The sequence is amino acids 30 to 340 from sp P49321-2(NASP_HUMAN Isoform 2) with a deletion of amino acids 101-159.
Source: (gene. exp.) Homo sapiens (human) / Gene: NASP
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P49321-2

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.79 Å3/Da / Density % sol: 74.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Calcium acetate, 0.1M HEPES (pH7.5), 40% v/v PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 3.287→40 Å / Num. obs: 9058 / % possible obs: 99.9 % / Redundancy: 33.2 % / Biso Wilson estimate: 122.4 Å2 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.035 / Rrim(I) all: 0.147 / Χ2: 0.394 / Net I/σ(I): 1.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Num. unique obsCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
3.3-3.4225.98700.5180.420.34399.8
3.42-3.5530.58690.9320.3240.357100
3.55-3.7233.28770.8950.2490.356100
3.72-3.9134.28740.9690.1560.3771000.9150.928
3.91-4.16329000.9840.0980.39499.90.5480.557
4.16-4.48378930.9950.0540.4171000.330.335
4.48-4.9337.28890.9980.0360.4241000.2210.224
4.93-5.6436.19220.9980.0350.4121000.2080.211
5.64-7.133.89300.9980.0230.4271000.1310.133
7.1-4031.8103410.0080.40199.80.0460.046

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.19refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NQ0

4nq0


Resolution: 3.287→39.178 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 29.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2609 674 7.49 %
Rwork0.2391 8326 -
obs0.2406 9000 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 215.19 Å2 / Biso mean: 131.8047 Å2 / Biso min: 88.63 Å2
Refinement stepCycle: final / Resolution: 3.287→39.178 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1740 0 0 0 1740
Num. residues----220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091763
X-RAY DIFFRACTIONf_angle_d0.8762368
X-RAY DIFFRACTIONf_chiral_restr0.046257
X-RAY DIFFRACTIONf_plane_restr0.005313
X-RAY DIFFRACTIONf_dihedral_angle_d6.0391079
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
3.2871-3.54080.33791180.34541610
3.5408-3.89680.29281410.26221602
3.8968-4.460.21511390.18931645
4.46-5.61650.2381580.21641646
5.6165-39.1780.27591180.24571823
Refinement TLS params.Method: refined / Origin x: 35.4341 Å / Origin y: -21.2588 Å / Origin z: 17.3432 Å
111213212223313233
T1.2554 Å2-0.0934 Å20.0762 Å2-1.1688 Å2-0.0692 Å2--1.1427 Å2
L0.2624 °2-0.1633 °2-0.7937 °2-0.4082 °2-1.0877 °2--2.0156 °2
S-0.0189 Å °-0.0094 Å °-0.0059 Å °-0.327 Å °-0.0137 Å °-0.0956 Å °0.9068 Å °-0.1441 Å °-0 Å °
Refinement TLS groupSelection details: all

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